You are right. There was only one Mirage in the Burgwies and the other was kept in one of the regular depots. Wartau is a workshop and there is not sufficient space for storage. I know there was a Mirage in Oerlikon depot for a while, but it may also have been in other locations in the meantime.
In fact the Burgwies museum is already too small to display the entire collection. Maybe they could if they filled every bit of track, but the museum concept is to have space so people can walk around the vehicles. Also by changing the collection around a couple of times a year, people have a reason to make multiple visits, and the idea is that they can also do themed exhibitions and displays from time to time.
Furthernore, the Tram Museum has a source of secondary income in renting out the museum for corporate entertainment and the like. Obviously this wouldn't work if there wasn't space.
So the arrangement now is that the museum at Burgwies holds a selection of working and non working trams, with further working trams kept in various depots as space allows (this is one of the reasons that it is always so difficult to add to the collection, VBZ doesn't have much spare depot space). Several non working cars are stored off system in a secure location. There is also a sizeable store of parts salavaged from scrapped trams, including large and heavy parts such as controllers, motors, axles and even a complete chassis/truck or two. This collection fills a building the size of a small depot. The collection also includes several buses and trolleybuses, which are easier to move and store than trams, but still need space somehow. The tram museum recently had to dispose of some of its buses in a rather controversial decision that led to a lot of anger. Fortunately the buses could all find new homes. But with space at a premium, this sort of thing can happen and could happen again. The collection also used to include an electric shunting loco which was standard gauge and used to shunt on industrial street tracks. It was on display outside Wartau for many years. That has been transferred to a private colection. They also had one of the cars of the old Polybahn and that is also now with a new owner.
I don't know how many Tram 2000s will be preserved. With space at a premium, there will have to be some tough decisons and I think that many variations will not be represented.